This is sometimes the nature of the beast. When your program is running you are doing DMA transfers to locations in memory that have been setup by your operating system. Now if you stop your program, with out killing or stopping the DAQ device it will cause you problems in some cases. You need to call AOClearWaveforms before you stop your program.
If you do not stop the DAQ device, before stopping your program it will cause the DAQ device to write to memory that is no longer allocated for that process. In most cases windows detects this as an error and reboots the system, because it thinks a program has crashed and is now writing to memory locations out of its designated space.
I hope this helps.
Joshua